Data regarding Musa genetics reveals certain types of has actually

BACs symbolizing each other distinctive line of loci hybridizing so you’re able to probes SbRPG661, SbRPG373 and SbRPG851 was indeed sequenced with the objective regarding relationship this new duration of replication prior to the newest divergence of your Musa and grain lineages

We also analyzed the 18,612 ginger (Zingiber officinale; Zingiberaceae, Zingiberales) EST-derived unigenes available on the TIGR Plant Transcript Assemblies web site (sequences generated by David Gang, University of Arizona) and found no evidence of large-scale duplication in the K_s distribution for paralogous pairs (Figure 8). Moreover, the modal K_s for reciprocal best matches between the Musa and Zingiber unigene sets is 0.78 (Figure 8), larger than the mode for Musa paralogous pairs. The age of the most recent common ancestor for the Musacaceae and Zingiberaceae is estimated at 87 Mya [3, 72, 73]. This implies an average synonymous substitution rate of 4.5 per 10 9 years (0.78 synonymous substitutions per site/(2*87,000,000 years)), intermediate between rates estimated for the Poaceae (6.1–6.5 per 10 9 years) and palms in the order Arecales (2.61 per 10 9 years; . We must emphasize that all of these rate estimates are approximate, based on rough estimates of minimum divergence times. However, regardless of ambiguities in substitution rate calibrations, our results indicate that the predicted large-scale duplication that occurred in the Musa lineage (K_s = 0.55) post-dates the divergence of lineages leading to Zingiber and Musa (K_s = 0.78), but occurred well before the separation of Musa A and Musa B (K_s = 0.0410).

K_s values were also computed on 1,034 pairs of homologous genes identified between the Musa ESTs and the rice genome sequences. As expected, the distribution of K_s values between rice-Musa homologs form a single peak centred around K_s = 1.7 (Figure 8). Using this K_s value to estimate the age of the Poales-Zingiberales split is less straightforward than described above for the Musa-Zingiber split, because synonymous substitution rates clearly vary between these Commelinid monocot lineages.

BAC fingerprint analyses revealed that whereas SbRPG854 hybridized to a single locus in the Musa genome, SbRPG probes SbRPG132 hybridized to 6 regions, SbRPG663 hybridized to 5 loci, and two loci were identified for SbRPG373, SbRPG661 and SbRPG851 (Table 1 and Additional file 1). linked here Pair-wise estimations of K_s, the number of synonymous substitutions per synonymous site, were 0.93 (± 0.25), 1.39 (± 0.19) and 1.43 (± 0.60) for Musa homologs of the coding regions of SbRPG661 (thioredoxin), SbRPG851 (phosphoglycerate kinase) and SbRPG373 (hypothetical protein), respectively. Phylogenetic analyses suggested that the SbRPG851 Musa homologs duplicated prior to the divergence of the Poales and the Zingiberales, (probably independent from the large-scale duplication described above), and the SbRPG661 and SbRPG373 Musa homologs are sister to each other in the gene tree, suggesting the duplications arose after the divergence of the Poales and the Zingiberales (data not shown).

We in addition to analyzed the degree of preservation anywhere between genomic regions related SbRPG661, SbRPG851 and you may SbRPG373 recurring family genes for the Musa and you can rice and discovered zero synteny within the nations secured because of the these homologs. Which lack of synteny was explained by the replication incidents and you can after that gene losings otherwise of the translocation of the focal genes.

Talk

step one.8 Mb out of Musa genomic sequence revealed that most of the BACs assessed were gene steeped having a minimal articles of transposable feature. Our analyses from 443 Musa genes forecast indicated that Musa genetics tend to have a “rice-like” bimodal GC shipment with a highly asymmetrical and you may long-tail toward highest GC stuff like in past knowledge [43, 44]. not, a moment family of “Arabidopsis-like” genes are located with an overall total lowest GC content no high gradient along side coding succession. Compared with a past assessment off lawn and non-lawn monocots [52, 53], all of our analyses suggest that Zingeberales genetics share some features on the genomes of each other eudicots and you may people in this new Poaceae. It results implies that the fresh Musa genome is more similar to cereal genomes in accordance with onion, asparagus therefore the basal-very monocot origin, Acorus.